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Pagnamenta AT, Yu J, Walker S, Noble AJ, Lord J, Dutta P, Hashim M, Camps C, Green H, Devaiah S, Nashef L, Parr J, Fratter C, Ibnouf Hussein R, Lindsay SJ, Lalloo F, Banos-Pinero B, Evans D, Mallin L, Waite A, Evans J, Newman A, Allen Z, Perez-Becerril C, Ryan G, Hart R, Taylor J, Bedenham T, Clement E, Blair E, Hay E, Forzano F, Higgs J, Canham N, Majumdar A, McEntagart M, Lahiri N, Stewart H, Smithson S, Calpena E, Jackson A, Banka S, Titheradge H, McGowan R, Rankin J, Shaw-Smith C, Evans DG, Burghel GJ, Smith MJ, Anderson E, Madhu R, Firth H, Ellard S, Brennan P, Anderson C, Taupin D, Rogers MT, Cook JA, Durkie M, East JE, Fowler D, Wilson L, Igbokwe R, Gardham A, Tomlinson I, Baralle D, Uhlig HH, Taylor JC. The impact of inversions across 33,924 families with rare disease from a national genome sequencing project. Am J Hum Genet 2024; 111:1140-1164. [PMID: 38776926 PMCID: PMC11179413 DOI: 10.1016/j.ajhg.2024.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Detection of structural variants (SVs) is currently biased toward those that alter copy number. The relative contribution of inversions toward genetic disease is unclear. In this study, we analyzed genome sequencing data for 33,924 families with rare disease from the 100,000 Genomes Project. From a database hosting >500 million SVs, we focused on 351 genes where haploinsufficiency is a confirmed disease mechanism and identified 47 ultra-rare rearrangements that included an inversion (24 bp to 36.4 Mb, 20/47 de novo). Validation utilized a number of orthogonal approaches, including retrospective exome analysis. RNA-seq data supported the respective diagnoses for six participants. Phenotypic blending was apparent in four probands. Diagnostic odysseys were a common theme (>50 years for one individual), and targeted analysis for the specific gene had already been performed for 30% of these individuals but with no findings. We provide formal confirmation of a European founder origin for an intragenic MSH2 inversion. For two individuals with complex SVs involving the MECP2 mutational hotspot, ambiguous SV structures were resolved using long-read sequencing, influencing clinical interpretation. A de novo inversion of HOXD11-13 was uncovered in a family with Kantaputra-type mesomelic dysplasia. Lastly, a complex translocation disrupting APC and involving nine rearranged segments confirmed a clinical diagnosis for three family members and resolved a conundrum for a sibling with a single polyp. Overall, inversions play a small but notable role in rare disease, likely explaining the etiology in around 1/750 families across heterogeneous clinical cohorts.
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Affiliation(s)
- Alistair T Pagnamenta
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Jing Yu
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK; Novo Nordisk Oxford Research Centre, Oxford, UK
| | | | - Alexandra J Noble
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Jenny Lord
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK; Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, UK
| | - Prasun Dutta
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Mona Hashim
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Carme Camps
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Hannah Green
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Smrithi Devaiah
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lina Nashef
- Department of Neurology, King's College Hospital, London, UK
| | - Jason Parr
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Carl Fratter
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Rana Ibnouf Hussein
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Sarah J Lindsay
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Benito Banos-Pinero
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - David Evans
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Lucy Mallin
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Adrian Waite
- Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - Julie Evans
- Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - Andrew Newman
- The All Wales Medical Genomics Service, University Hospital of Wales, Cardiff, UK
| | - Zoe Allen
- North Thames Rare and Inherited Disease Laboratory, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Cristina Perez-Becerril
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Gavin Ryan
- West Midlands Regional Genetics Laboratory, Central and South Genomic Laboratory Hub, Birmingham, UK
| | - Rachel Hart
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - John Taylor
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Tina Bedenham
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Emma Clement
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Ed Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Eleanor Hay
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Francesca Forzano
- Clinical Genetics Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jenny Higgs
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Natalie Canham
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Anirban Majumdar
- Department of Paediatric Neurology, Bristol Children's Hospital, Bristol, UK
| | - Meriel McEntagart
- SW Thames Centre for Genomic Medicine, University of London & St George's University Hospitals NHS Foundation Trust, St George's, London, UK
| | - Nayana Lahiri
- SW Thames Centre for Genomic Medicine, University of London & St George's University Hospitals NHS Foundation Trust, St George's, London, UK
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sarah Smithson
- Department of Clinical Genetics, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Unidad CIBERER (CB06/07/1030), Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Adam Jackson
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Hannah Titheradge
- Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Ruth McGowan
- West of Scotland Centre for Genomic Medicine, Glasgow, UK
| | - Julia Rankin
- Department of Clinical Genetics, Royal Devon University Healthcare NHS Trust, Exeter, UK
| | - Charles Shaw-Smith
- Department of Clinical Genetics, Royal Devon University Healthcare NHS Trust, Exeter, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Miriam J Smith
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Emily Anderson
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Rajesh Madhu
- Paediatric Neurosciences Department, Alder Hey Children's Hospital NHS Foundation Trust, Liverpool, UK
| | - Helen Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sian Ellard
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Paul Brennan
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle University, Newcastle, UK
| | - Claire Anderson
- Canberra Clinical Genomics, Canberra Health Services and The Australian National University, Canberra, ACT, Australia
| | - Doug Taupin
- Cancer Research, Canberra Hospital, Canberra, ACT, Australia
| | - Mark T Rogers
- The All Wales Medical Genomics Service, University Hospital of Wales, Cardiff, UK
| | - Jackie A Cook
- Department of Clinical Genetics, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, North East and Yorkshire Genomic Laboratory Hub, Sheffield, UK
| | - James E East
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Darren Fowler
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Louise Wilson
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Rebecca Igbokwe
- Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Alice Gardham
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Ian Tomlinson
- Department of Oncology, University of Oxford, Oxford, UK
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Holm H Uhlig
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Jenny C Taylor
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK.
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2
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Munro V, Kelly V, Messner CB, Kustatscher G. Cellular control of protein levels: A systems biology perspective. Proteomics 2024; 24:e2200220. [PMID: 38012370 DOI: 10.1002/pmic.202200220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
How cells regulate protein levels is a central question of biology. Over the past decades, molecular biology research has provided profound insights into the mechanisms and the molecular machinery governing each step of the gene expression process, from transcription to protein degradation. Recent advances in transcriptomics and proteomics have complemented our understanding of these fundamental cellular processes with a quantitative, systems-level perspective. Multi-omic studies revealed significant quantitative, kinetic and functional differences between the genome, transcriptome and proteome. While protein levels often correlate with mRNA levels, quantitative investigations have demonstrated a substantial impact of translation and protein degradation on protein expression control. In addition, protein-level regulation appears to play a crucial role in buffering protein abundances against undesirable mRNA expression variation. These findings have practical implications for many fields, including gene function prediction and precision medicine.
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Affiliation(s)
- Victoria Munro
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Van Kelly
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Christoph B Messner
- Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Georg Kustatscher
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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3
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Gonzalez P, Hauck QC, Baxevanis AD. Conserved Noncoding Elements Evolve Around the Same Genes Throughout Metazoan Evolution. Genome Biol Evol 2024; 16:evae052. [PMID: 38502060 PMCID: PMC10988421 DOI: 10.1093/gbe/evae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 03/07/2024] [Accepted: 03/13/2024] [Indexed: 03/20/2024] Open
Abstract
Conserved noncoding elements (CNEs) are DNA sequences located outside of protein-coding genes that can remain under purifying selection for up to hundreds of millions of years. Studies in vertebrate genomes have revealed that most CNEs carry out regulatory functions. Notably, many of them are enhancers that control the expression of homeodomain transcription factors and other genes that play crucial roles in embryonic development. To further our knowledge of CNEs in other parts of the animal tree, we conducted a large-scale characterization of CNEs in more than 50 genomes from three of the main branches of the metazoan tree: Cnidaria, Mollusca, and Arthropoda. We identified hundreds of thousands of CNEs and reconstructed the temporal dynamics of their appearance in each lineage, as well as determining their spatial distribution across genomes. We show that CNEs evolve repeatedly around the same genes across the Metazoa, including around homeodomain genes and other transcription factors; they also evolve repeatedly around genes involved in neural development. We also show that transposons are a major source of CNEs, confirming previous observations from vertebrates and suggesting that they have played a major role in wiring developmental gene regulatory mechanisms since the dawn of animal evolution.
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Affiliation(s)
- Paul Gonzalez
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Quinn C Hauck
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andreas D Baxevanis
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Hintermann A, Bolt CC, Hawkins MB, Valentin G, Lopez-Delisle L, Gitto S, Gómez PB, Mascrez B, Mansour TA, Nakamura T, Harris MP, Shubin NH, Duboule D. EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE DURING THE EMERGENCE OF DIGITS AND GENITALS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.24.586442. [PMID: 38585989 PMCID: PMC10996561 DOI: 10.1101/2024.03.24.586442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The transition from fins to limbs has been a rich source of discussion for more than a century. One open and important issue is understanding how the mechanisms that pattern digits arose during vertebrate evolution. In this context, the analysis of Hox gene expression and functions to infer evolutionary scenarios has been a productive approach to explain the changes in organ formation, particularly in limbs. In tetrapods, the transcription of Hoxd genes in developing digits depends on a well-characterized set of enhancers forming a large regulatory landscape1,2. This control system has a syntenic counterpart in zebrafish, even though they lack bona fide digits, suggestive of deep homology3 between distal fin and limb developmental mechanisms. We tested the global function of this landscape to assess ancestry and source of limb and fin variation. In contrast to results in mice, we show here that the deletion of the homologous control region in zebrafish has a limited effect on the transcription of hoxd genes during fin development. However, it fully abrogates hoxd expression within the developing cloaca, an ancestral structure related to the mammalian urogenital sinus. We show that similar to the limb, Hoxd gene function in the urogenital sinus of the mouse also depends on enhancers located in this same genomic domain. Thus, we conclude that the current regulation underlying Hoxd gene expression in distal limbs was co-opted in tetrapods from a preexisting cloacal program. The orthologous chromatin domain in fishes may illustrate a rudimentary or partial step in this evolutionary co-option.
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Affiliation(s)
- Aurélie Hintermann
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
| | - Christopher Chase Bolt
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
| | - M. Brent Hawkins
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA, Department of Orthopedic Research, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Guillaume Valentin
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
| | - Sandra Gitto
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
| | - Paula Barrera Gómez
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
| | | | - Tetsuya Nakamura
- Department of Genetics, Rutgers University, New Brunswick, NJ, USA
| | - Matthew P. Harris
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA, Department of Orthopedic Research, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Neil H. Shubin
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
- Center for Interdisciplinary Research in Biology CIRB, Collège de France, CNRS, INSERM, Université PSL, Paris, France
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Mañes-García J, Marco-Ferreres R, Beccari L. Shaping gene expression and its evolution by chromatin architecture and enhancer activity. Curr Top Dev Biol 2024; 159:406-437. [PMID: 38729683 DOI: 10.1016/bs.ctdb.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
Transcriptional regulation plays a pivotal role in orchestrating the intricate genetic programs governing embryonic development. The expression of developmental genes relies on the combined activity of several cis-regulatory elements (CREs), such as enhancers and silencers, which can be located at long linear distances from the genes that they regulate and that interact with them through establishment of chromatin loops. Mutations affecting their activity or interaction with their target genes can lead to developmental disorders and are thought to have importantly contributed to the evolution of the animal body plan. The income of next-generation-sequencing approaches has allowed identifying over a million of sequences with putative regulatory potential in the human genome. Characterizing their function and establishing gene-CREs maps is essential to decode the logic governing developmental gene expression and is one of the major challenges of the post-genomic era. Chromatin 3D organization plays an essential role in determining how CREs specifically contact their target genes while avoiding deleterious off-target interactions. Our understanding of these aspects has greatly advanced with the income of chromatin conformation capture techniques and fluorescence microscopy approaches to visualize the organization of DNA elements in the nucleus. Here we will summarize relevant aspects of how the interplay between CRE activity and chromatin 3D organization regulates developmental gene expression and how it relates to pathological conditions and the evolution of animal body plan.
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Affiliation(s)
| | | | - Leonardo Beccari
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain.
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Wilderman A, D'haene E, Baetens M, Yankee TN, Winchester EW, Glidden N, Roets E, Van Dorpe J, Janssens S, Miller DE, Galey M, Brown KM, Stottmann RW, Vergult S, Weaver KN, Brugmann SA, Cox TC, Cotney J. A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development. Nat Commun 2024; 15:136. [PMID: 38167838 PMCID: PMC10762089 DOI: 10.1038/s41467-023-44506-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Craniofacial abnormalities account for approximately one third of birth defects. The regulatory programs that build the face require precisely controlled spatiotemporal gene expression, achieved through tissue-specific enhancers. Clusters of coactivated enhancers and their target genes, known as superenhancers, are important in determining cell identity but have been largely unexplored in development. In this study we identified superenhancer regions unique to human embryonic craniofacial tissue. To demonstrate the importance of such regions in craniofacial development and disease, we focused on an ~600 kb noncoding region located between NPVF and NFE2L3. We identified long range interactions with this region in both human and mouse embryonic craniofacial tissue with the anterior portion of the HOXA gene cluster. Mice lacking this superenhancer exhibit perinatal lethality, and present with highly penetrant skull defects and orofacial clefts phenocopying Hoxa2-/- mice. Moreover, we identified two cases of de novo copy number changes of the superenhancer in humans both with severe craniofacial abnormalities. This evidence suggests we have identified a critical noncoding locus control region that specifically regulates anterior HOXA genes and copy number changes are pathogenic in human patients.
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Affiliation(s)
| | - Eva D'haene
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Machteld Baetens
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Emma Wentworth Winchester
- Graduate Program UConn Health, Farmington, CT, USA
- University of Connecticut School of Dental Medicine, Farmington, CT, USA
| | - Nicole Glidden
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Ellen Roets
- Department of Obstetrics, Women's Clinic, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Sandra Janssens
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Danny E Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Washington, WA, USA
- Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Brotman Baty Institute of Precision Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Miranda Galey
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Washington, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Kari M Brown
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Rolf W Stottmann
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University School of Medicine, Columbus, OH, USA
| | - Sarah Vergult
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - K Nicole Weaver
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Samantha A Brugmann
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Timothy C Cox
- Department of Oral & Craniofacial Sciences, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pediatrics, University of Missouri Kansas City, Kansas City, MO, USA
| | - Justin Cotney
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA.
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
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7
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Abstract
Enhancers are cis-regulatory elements that can stimulate gene expression from distance, and drive precise spatiotemporal gene expression profiles during development. Functional enhancers display specific features including an open chromatin conformation, Histone H3 lysine 27 acetylation, Histone H3 lysine 4 mono-methylation enrichment, and enhancer RNAs production. These features are modified upon developmental cues which impacts their activity. In this review, we describe the current state of knowledge about enhancer functions and the diverse chromatin signatures found on enhancers. We also discuss the dynamic changes of enhancer chromatin signatures, and their impact on lineage specific gene expression profiles, during development or cellular differentiation.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,CONTACT Amandine Barral Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. 3400 Civic Blvd, Philadelphia, Pennsylvania19104, USA
| | - Jérôme Déjardin
- Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, Montpellier, France,Jérôme Déjardin Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier34000, France
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8
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Preston AE, Frost JN, Badat M, Teh M, Armitage AE, Norfo R, Wideman SK, Hanifi M, White N, Roy N, Ghesquiere B, Babbs C, Kassouf M, Davies J, Hughes JR, Beagrie R, Higgs DR, Drakesmith H. Ancient genomic linkage couples metabolism with erythroid development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.558944. [PMID: 37808769 PMCID: PMC10557585 DOI: 10.1101/2023.09.25.558944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Generation of mature cells from progenitors requires tight coupling of differentiation and metabolism. During erythropoiesis, erythroblasts are required to massively upregulate globin synthesis then clear extraneous material and enucleate to produce erythrocytes1-3. Nprl3 has remained in synteny with the α-globin genes for >500 million years4, and harbours the majority of the α-globin enhancers5. Nprl3 is a highly conserved inhibitor of mTORC1, which controls cellular metabolism. However, whether Nprl3 itself serves an erythroid role is unknown. Here, we show that Nprl3 is a key regulator of erythroid metabolism. Using Nprl3-deficient fetal liver and adult competitive bone marrow - fetal liver chimeras, we show that NprI3 is required for sufficient erythropoiesis. Loss of Nprl3 elevates mTORC1 signalling, suppresses autophagy and disrupts erythroblast glycolysis and redox control. Human CD34+ progenitors lacking NPRL3 produce fewer enucleated cells and demonstrate dysregulated mTORC1 signalling in response to nutrient availability and erythropoietin. Finally, we show that the α-globin enhancers upregulate NprI3 expression, and that this activity is necessary for optimal erythropoiesis. Therefore, the anciently conserved linkage of NprI3, α-globin and their associated enhancers has enabled coupling of metabolic and developmental control in erythroid cells. This may enable erythropoiesis to adapt to fluctuating nutritional and environmental conditions.
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Affiliation(s)
- Alexandra E Preston
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Joe N Frost
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Mohsin Badat
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Megan Teh
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Andrew E Armitage
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ruggiero Norfo
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Sarah K Wideman
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Muhammad Hanifi
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Natasha White
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Noémi Roy
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Bart Ghesquiere
- Metabolomics Expertise Center, VIB Center for Cancer Biology, 3000 Leuven, Belgium
- Metabolomics Expertise Center, Department of Oncology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Mira Kassouf
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - James Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Rob Beagrie
- Chromatin and Disease Group, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Hal Drakesmith
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
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9
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Komatsu V, Cooper B, Yim P, Chan K, Gong W, Wheatley L, Rohs R, Fraser SE, Trinh LA. Hand2 represses non-cardiac cell fates through chromatin remodeling at cis- regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.23.559156. [PMID: 37790542 PMCID: PMC10542161 DOI: 10.1101/2023.09.23.559156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Developmental studies have revealed the importance of the transcription factor Hand2 in cardiac development. Hand2 promotes cardiac progenitor differentiation and epithelial maturation, while repressing other tissue types. The mechanisms underlying the promotion of cardiac fates are far better understood than those underlying the repression of alternative fates. Here, we assess Hand2-dependent changes in gene expression and chromatin remodeling in cardiac progenitors of zebrafish embryos. Cell-type specific transcriptome analysis shows a dual function for Hand2 in activation of cardiac differentiation genes and repression of pronephric pathways. We identify functional cis- regulatory elements whose chromatin accessibility are increased in hand2 mutant cells. These regulatory elements associate with non-cardiac gene expression, and drive reporter gene expression in tissues associated with Hand2-repressed genes. We find that functional Hand2 is sufficient to reduce non-cardiac reporter expression in cardiac lineages. Taken together, our data support a model of Hand2-dependent coordination of transcriptional programs, not only through transcriptional activation of cardiac and epithelial maturation genes, but also through repressive chromatin remodeling at the DNA regulatory elements of non-cardiac genes.
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10
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Abstract
Hox genes encode evolutionarily conserved transcription factors that are essential for the proper development of bilaterian organisms. Hox genes are unique because they are spatially and temporally regulated during development in a manner that is dictated by their tightly linked genomic organization. Although their genetic function during embryonic development has been interrogated, less is known about how these transcription factors regulate downstream genes to direct morphogenetic events. Moreover, the continued expression and function of Hox genes at postnatal and adult stages highlights crucial roles for these genes throughout the life of an organism. Here, we provide an overview of Hox genes, highlighting their evolutionary history, their unique genomic organization and how this impacts the regulation of their expression, what is known about their protein structure, and their deployment in development and beyond.
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Affiliation(s)
- Katharine A. Hubert
- Program in Genetics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Deneen M. Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
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11
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Wucherpfennig JI, Howes TR, Au JN, Au EH, Roberts Kingman GA, Brady SD, Herbert AL, Reimchen TE, Bell MA, Lowe CB, Dalziel AC, Kingsley DM. Evolution of stickleback spines through independent cis-regulatory changes at HOXDB. Nat Ecol Evol 2022; 6:1537-1552. [PMID: 36050398 PMCID: PMC9525239 DOI: 10.1038/s41559-022-01855-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/19/2022] [Indexed: 11/10/2022]
Abstract
Understanding the mechanisms leading to new traits or additional features in organisms is a fundamental goal of evolutionary biology. We show that HOXDB regulatory changes have been used repeatedly in different fish genera to alter the length and number of the prominent dorsal spines used to classify stickleback species. In Gasterosteus aculeatus (typically 'three-spine sticklebacks'), a variant HOXDB allele is genetically linked to shortening an existing spine and adding an additional spine. In Apeltes quadracus (typically 'four-spine sticklebacks'), a variant HOXDB allele is associated with lengthening a spine and adding an additional spine in natural populations. The variant alleles alter the same non-coding enhancer region in the HOXDB locus but do so by diverse mechanisms, including single-nucleotide polymorphisms, deletions and transposable element insertions. The independent regulatory changes are linked to anterior expansion or contraction of HOXDB expression. We propose that associated changes in spine lengths and numbers are partial identity transformations in a repeating skeletal series that forms major defensive structures in fish. Our findings support the long-standing hypothesis that natural Hox gene variation underlies key patterning changes in wild populations and illustrate how different mutational mechanisms affecting the same region may produce opposite gene expression changes with similar phenotypic outcomes.
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Affiliation(s)
- Julia I Wucherpfennig
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Timothy R Howes
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jessica N Au
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Eric H Au
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | | | - Shannon D Brady
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Amy L Herbert
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas E Reimchen
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, CA, USA
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Anne C Dalziel
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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12
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Pinglay S, Bulajić M, Rahe DP, Huang E, Brosh R, Mamrak NE, King BR, German S, Cadley JA, Rieber L, Easo N, Lionnet T, Mahony S, Maurano MT, Holt LJ, Mazzoni EO, Boeke JD. Synthetic regulatory reconstitution reveals principles of mammalian Hox cluster regulation. Science 2022; 377:eabk2820. [PMID: 35771912 PMCID: PMC9648154 DOI: 10.1126/science.abk2820] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Precise Hox gene expression is crucial for embryonic patterning. Intra-Hox transcription factor binding and distal enhancer elements have emerged as the major regulatory modules controlling Hox gene expression. However, quantifying their relative contributions has remained elusive. Here, we introduce "synthetic regulatory reconstitution," a conceptual framework for studying gene regulation, and apply it to the HoxA cluster. We synthesized and delivered variant rat HoxA clusters (130 to 170 kilobases) to an ectopic location in the mouse genome. We found that a minimal HoxA cluster recapitulated correct patterns of chromatin remodeling and transcription in response to patterning signals, whereas the addition of distal enhancers was needed for full transcriptional output. Synthetic regulatory reconstitution could provide a generalizable strategy for deciphering the regulatory logic of gene expression in complex genomes.
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Affiliation(s)
- Sudarshan Pinglay
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Milica Bulajić
- Department of Biology, New York University, New York, NY 10003, USA
| | - Dylan P. Rahe
- Department of Biology, New York University, New York, NY 10003, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Ran Brosh
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Nicholas E. Mamrak
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Benjamin R. King
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Sergei German
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - John A. Cadley
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Lila Rieber
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Nicole Easo
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Timothée Lionnet
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Cell Biology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew T. Maurano
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Liam J. Holt
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | | | - Jef D. Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
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13
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Context-dependent enhancer function revealed by targeted inter-TAD relocation. Nat Commun 2022; 13:3488. [PMID: 35715427 PMCID: PMC9205857 DOI: 10.1038/s41467-022-31241-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/09/2022] [Indexed: 11/08/2022] Open
Abstract
The expression of some genes depends on large, adjacent regions of the genome that contain multiple enhancers. These regulatory landscapes frequently align with Topologically Associating Domains (TADs), where they integrate the function of multiple similar enhancers to produce a global, TAD-specific regulation. We asked if an individual enhancer could overcome the influence of one of these landscapes, to drive gene transcription. To test this, we transferred an enhancer from its native location, into a nearby TAD with a related yet different functional specificity. We used the biphasic regulation of Hoxd genes during limb development as a paradigm. These genes are first activated in proximal limb cells by enhancers located in one TAD, which is then silenced when the neighboring TAD activates its enhancers in distal limb cells. We transferred a distal limb enhancer into the proximal limb TAD and found that its new context suppresses its normal distal specificity, even though it is bound by HOX13 transcription factors, which are responsible for the distal activity. This activity can be rescued only when a large portion of the surrounding environment is removed. These results indicate that, at least in some cases, the functioning of enhancer elements is subordinated to the host chromatin context, which can exert a dominant control over its activity. Here the authors show that a strong enhancer sequence can be controlled by the chromatin environment provided by a topologically associated domain (TAD) located nearby. An enhancer relocated by homologous recombination takes all the hallmarks of its new neighboring enhancers located in the recipient TAD.
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14
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Hintermann A, Guerreiro I, Lopez-Delisle L, Bolt CC, Gitto S, Duboule D, Beccari L. Developmental and evolutionary comparative analysis of a regulatory landscape in mouse and chicken. Development 2022; 149:275867. [PMID: 35770682 PMCID: PMC9307994 DOI: 10.1242/dev.200594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/23/2022] [Indexed: 12/12/2022]
Abstract
Modifications in gene regulation are driving forces in the evolution of organisms. Part of these changes involve cis-regulatory elements (CREs), which contact their target genes through higher-order chromatin structures. However, how such architectures and variations in CREs contribute to transcriptional evolvability remains elusive. We use Hoxd genes as a paradigm for the emergence of regulatory innovations, as many relevant enhancers are located in a regulatory landscape highly conserved in amniotes. Here, we analysed their regulation in murine vibrissae and chicken feather primordia, two skin appendages expressing different Hoxd gene subsets, and compared the regulation of these genes in these appendages with that in the elongation of the posterior trunk. In the two former structures, distinct subsets of Hoxd genes are contacted by different lineage-specific enhancers, probably as a result of using an ancestral chromatin topology as an evolutionary playground, whereas the gene regulation that occurs in the mouse and chicken embryonic trunk partially relies on conserved CREs. A high proportion of these non-coding sequences active in the trunk have functionally diverged between species, suggesting that transcriptional robustness is maintained, despite considerable divergence in enhancer sequences. Summary: Analyses of the relationships between chromatin architecture and regulatory activities at the HoxD locus show that ancestral transcription patterns can be maintained while new regulations evolve.
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Affiliation(s)
- Aurélie Hintermann
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Isabel Guerreiro
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Lucille Lopez-Delisle
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
| | - Christopher Chase Bolt
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
| | - Sandra Gitto
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Denis Duboule
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
- Collège de France 3 , 11 Place Marcelin Berthelot, 75005 Paris , France
| | - Leonardo Beccari
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
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15
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Kaplow IM, Schäffer DE, Wirthlin ME, Lawler AJ, Brown AR, Kleyman M, Pfenning AR. Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin. BMC Genomics 2022; 23:291. [PMID: 35410163 PMCID: PMC8996547 DOI: 10.1186/s12864-022-08450-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Evolutionary conservation is an invaluable tool for inferring functional significance in the genome, including regions that are crucial across many species and those that have undergone convergent evolution. Computational methods to test for sequence conservation are dominated by algorithms that examine the ability of one or more nucleotides to align across large evolutionary distances. While these nucleotide alignment-based approaches have proven powerful for protein-coding genes and some non-coding elements, they fail to capture conservation of many enhancers, distal regulatory elements that control spatial and temporal patterns of gene expression. The function of enhancers is governed by a complex, often tissue- and cell type-specific code that links combinations of transcription factor binding sites and other regulation-related sequence patterns to regulatory activity. Thus, function of orthologous enhancer regions can be conserved across large evolutionary distances, even when nucleotide turnover is high. RESULTS We present a new machine learning-based approach for evaluating enhancer conservation that leverages the combinatorial sequence code of enhancer activity rather than relying on the alignment of individual nucleotides. We first train a convolutional neural network model that can predict tissue-specific open chromatin, a proxy for enhancer activity, across mammals. Next, we apply that model to distinguish instances where the genome sequence would predict conserved function versus a loss of regulatory activity in that tissue. We present criteria for systematically evaluating model performance for this task and use them to demonstrate that our models accurately predict tissue-specific conservation and divergence in open chromatin between primate and rodent species, vastly out-performing leading nucleotide alignment-based approaches. We then apply our models to predict open chromatin at orthologs of brain and liver open chromatin regions across hundreds of mammals and find that brain enhancers associated with neuron activity have a stronger tendency than the general population to have predicted lineage-specific open chromatin. CONCLUSION The framework presented here provides a mechanism to annotate tissue-specific regulatory function across hundreds of genomes and to study enhancer evolution using predicted regulatory differences rather than nucleotide-level conservation measurements.
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Affiliation(s)
- Irene M Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA. .,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Daniel E Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Morgan E Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alyssa J Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA.,Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ashley R Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Michael Kleyman
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Andreas R Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA. .,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA. .,Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA.
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16
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Essay the (unusual) heuristic value of Hox gene clusters; a matter of time? Dev Biol 2022; 484:75-87. [PMID: 35182536 DOI: 10.1016/j.ydbio.2022.02.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/22/2022]
Abstract
Ever since their first report in 1984, Antennapedia-type homeobox (Hox) genes have been involved in such a series of interesting observations, in particular due to their conserved clustered organization between vertebrates and arthropods, that one may legitimately wonder about the origin of this heuristic value. In this essay, I first consider different examples where Hox gene clusters have been instrumental in providing conceptual advances, taken from various fields of research and mostly involving vertebrate embryos. These examples touch upon our understanding of genomic evolution, the revisiting of 19th century views on the relationships between development and evolution and the building of a new framework to understand long-range and pleiotropic gene regulation during development. I then discuss whether the high value of the Hox gene family, when considered as an epistemic object, is related to its clustered structure (and the absence thereof in some animal species) and, if so, what is it in such particular genetic oddities that made them so generous in providing the scientific community with interesting information.
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17
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Transcriptional Regulation and Implications for Controlling Hox Gene Expression. J Dev Biol 2022; 10:jdb10010004. [PMID: 35076545 PMCID: PMC8788451 DOI: 10.3390/jdb10010004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/06/2023] Open
Abstract
Hox genes play key roles in axial patterning and regulating the regional identity of cells and tissues in a wide variety of animals from invertebrates to vertebrates. Nested domains of Hox expression generate a combinatorial code that provides a molecular framework for specifying the properties of tissues along the A–P axis. Hence, it is important to understand the regulatory mechanisms that coordinately control the precise patterns of the transcription of clustered Hox genes required for their roles in development. New insights are emerging about the dynamics and molecular mechanisms governing transcriptional regulation, and there is interest in understanding how these may play a role in contributing to the regulation of the expression of the clustered Hox genes. In this review, we summarize some of the recent findings, ideas and emerging mechanisms underlying the regulation of transcription in general and consider how they may be relevant to understanding the transcriptional regulation of Hox genes.
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18
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Jia W, Zhou X, Guo N, Zhang D, Hou M, Luo Y, Peng X, Yang X, Zhang X. A novel microdeletion upstream of HOXD13 in a Chinese family with synpolydactyly. Am J Med Genet A 2021; 188:31-36. [PMID: 34467619 DOI: 10.1002/ajmg.a.62480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 08/07/2021] [Accepted: 08/13/2021] [Indexed: 11/06/2022]
Abstract
Synpolydactyly (SPD) is a digital malformation with the typical clinical phenotype of the webbing of 3/4 fingers and/or 4/5 toes, and combined with polydactyly. In this study, we investigated a Chinese family with SPD and genetic analysis found that all of the affected individuals in the family carry a heterozygous 11,451 bp microdeletion at chr2:176933872-176945322 (GRCh37), which is located upstream of HOXD13 gene, the known disease gene for SPD1. All the affected individuals in the family carry the heterozygous deletion variant, and the variant co-segregated with SPD in the family. Thus, we speculate that the 11,451 bp microdeletion is the disease-causing variant in the family. To date, the microdeletion associating with SPD1 which we identified is the smallest deletion upstream of the HOXD13 gene and not altering the sequence of the HOXD13 gene.
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Affiliation(s)
- Weimin Jia
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaopei Zhou
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Naiqiang Guo
- Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Dazhi Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Meiqi Hou
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yalin Luo
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xuejie Peng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xue Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xianqin Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, Hubei, China
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19
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Bolt CC, Lopez-Delisle L, Mascrez B, Duboule D. Mesomelic dysplasias associated with the HOXD locus are caused by regulatory reallocations. Nat Commun 2021; 12:5013. [PMID: 34408147 PMCID: PMC8373931 DOI: 10.1038/s41467-021-25330-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/05/2021] [Indexed: 02/07/2023] Open
Abstract
Human families with chromosomal rearrangements at 2q31, where the human HOXD locus maps, display mesomelic dysplasia, a severe shortening and bending of the limb. In mice, the dominant Ulnaless inversion of the HoxD cluster produces a similar phenotype suggesting the same origin for these malformations in humans and mice. Here we engineer 1 Mb inversion including the HoxD gene cluster, which positioned Hoxd13 close to proximal limb enhancers. Using this model, we show that these enhancers contact and activate Hoxd13 in proximal cells, inducing the formation of mesomelic dysplasia. We show that a secondary Hoxd13 null mutation in-cis with the inversion completely rescues the alterations, demonstrating that ectopic HOXD13 is directly responsible for this bone anomaly. Single-cell expression analysis and evaluation of HOXD13 binding sites suggests that the phenotype arises primarily by acting through genes normally controlled by HOXD13 in distal limb cells. Altogether, these results provide a conceptual and mechanistic framework to understand and unify the molecular origins of human mesomelic dysplasia associated with 2q31.
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MESH Headings
- Abnormalities, Multiple/embryology
- Abnormalities, Multiple/genetics
- Abnormalities, Multiple/metabolism
- Animals
- Bone Diseases, Developmental/embryology
- Bone Diseases, Developmental/genetics
- Bone Diseases, Developmental/metabolism
- Disease Models, Animal
- Female
- Gene Deletion
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Limb Deformities, Congenital/embryology
- Limb Deformities, Congenital/genetics
- Limb Deformities, Congenital/metabolism
- Loss of Function Mutation
- Male
- Mice, Inbred C57BL
- Multigene Family
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Mice
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Affiliation(s)
- Christopher Chase Bolt
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
- Collège de France, Paris, France.
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20
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Conserved Mechanisms, Novel Anatomies: The Developmental Basis of Fin Evolution and the Origin of Limbs. DIVERSITY 2021. [DOI: 10.3390/d13080384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The transformation of paired fins into tetrapod limbs is one of the most intensively scrutinized events in animal evolution. Early anatomical and embryological datasets identified distinctive morphological regions within the appendage and posed hypotheses about how the loss, gain, and transformation of these regions could explain the observed patterns of both extant and fossil appendage diversity. These hypotheses have been put to the test by our growing understanding of patterning mechanisms that regulate formation of the appendage axes, comparisons of gene expression data from an array of phylogenetically informative taxa, and increasingly sophisticated and elegant experiments leveraging the latest molecular approaches. Together, these data demonstrate the remarkable conservation of developmental mechanisms, even across phylogenetically and morphologically disparate taxa, as well as raising new questions about the way we view homology, evolutionary novelty, and the often non-linear connection between morphology and gene expression. In this review, we present historical hypotheses regarding paired fin evolution and limb origins, summarize key aspects of central appendage patterning mechanisms in model and non-model species, address how modern comparative developmental data interface with our understanding of appendage anatomy, and highlight new approaches that promise to provide new insight into these well-traveled questions.
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21
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Tena JJ, Santos-Pereira JM. Topologically Associating Domains and Regulatory Landscapes in Development, Evolution and Disease. Front Cell Dev Biol 2021; 9:702787. [PMID: 34295901 PMCID: PMC8290416 DOI: 10.3389/fcell.2021.702787] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/17/2021] [Indexed: 01/02/2023] Open
Abstract
Animal genomes are folded in topologically associating domains (TADs) that have been linked to the regulation of the genes they contain by constraining regulatory interactions between cis-regulatory elements and promoters. Therefore, TADs are proposed as structural scaffolds for the establishment of regulatory landscapes (RLs). In this review, we discuss recent advances in the connection between TADs and gene regulation, their relationship with gene RLs and their dynamics during development and differentiation. Moreover, we describe how restructuring TADs may lead to pathological conditions, which explains their high evolutionary conservation, but at the same time it provides a substrate for the emergence of evolutionary innovations that lay at the origin of vertebrates and other phylogenetic clades.
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Affiliation(s)
- Juan J. Tena
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - José M. Santos-Pereira
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
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22
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Razin SV, Ioudinkova ES, Kantidze OL, Iarovaia OV. Co-Regulated Genes and Gene Clusters. Genes (Basel) 2021; 12:907. [PMID: 34208174 PMCID: PMC8230824 DOI: 10.3390/genes12060907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/27/2022] Open
Abstract
There are many co-regulated genes in eukaryotic cells. The coordinated activation or repression of such genes occurs at specific stages of differentiation, or under the influence of external stimuli. As a rule, co-regulated genes are dispersed in the genome. However, there are also gene clusters, which contain paralogous genes that encode proteins with similar functions. In this aspect, they differ significantly from bacterial operons containing functionally linked genes that are not paralogs. In this review, we discuss the reasons for the existence of gene clusters in vertebrate cells and propose that clustering is necessary to ensure the possibility of selective activation of one of several similar genes.
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Affiliation(s)
- Sergey V. Razin
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Elena S. Ioudinkova
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
| | - Omar L. Kantidze
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
| | - Olga V. Iarovaia
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
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23
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Mammalian-specific ectodermal enhancers control the expression of Hoxc genes in developing nails and hair follicles. Proc Natl Acad Sci U S A 2020; 117:30509-30519. [PMID: 33199643 PMCID: PMC7720164 DOI: 10.1073/pnas.2011078117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Vertebrate Hox genes are critical for the establishment of structures during the development of the main body axis. Subsequently, they play important roles either in organizing secondary axial structures such as the appendages, or during homeostasis in postnatal stages and adulthood. Here, we set up to analyze their elusive function in the ectodermal compartment, using the mouse limb bud as a model. We report that the HoxC gene cluster was co-opted to be transcribed in the distal limb ectoderm, where it is activated following the rule of temporal colinearity. These ectodermal cells subsequently produce various keratinized organs such as nails or claws. Accordingly, deletion of the HoxC cluster led to mice lacking nails (anonychia), a condition stronger than the previously reported loss of function of Hoxc13, which is the causative gene of the ectodermal dysplasia 9 (ECTD9) in human patients. We further identified two mammalian-specific ectodermal enhancers located upstream of the HoxC gene cluster, which together regulate Hoxc gene expression in the hair and nail ectodermal organs. Deletion of these regulatory elements alone or in combination revealed a strong quantitative component in the regulation of Hoxc genes in the ectoderm, suggesting that these two enhancers may have evolved along with the mammalian taxon to provide the level of HOXC proteins necessary for the full development of hair and nail.
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24
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Kriechbaumer V, Brandizzi F. The plant endoplasmic reticulum: an organized chaos of tubules and sheets with multiple functions. J Microsc 2020; 280:122-133. [PMID: 32426862 PMCID: PMC10895883 DOI: 10.1111/jmi.12909] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022]
Abstract
The endoplasmic reticulum is a fascinating organelle at the core of the secretory pathway. It is responsible for the synthesis of one third of the cellular proteome and, in plant cells, it produces receptors and transporters of hormones as well as the proteins responsible for the biosynthesis of critical components of a cellulosic cell wall. The endoplasmic reticulum structure resembles a spider-web network of interconnected tubules and cisternae that pervades the cell. The study of the dynamics and interaction of this organelles with other cellular structures such as the plasma membrane, the Golgi apparatus and the cytoskeleton, have been permitted by the implementation of fluorescent protein and advanced confocal imaging. In this review, we report on the findings that contributed towards the understanding of the endoplasmic reticulum morphology and function with the aid of fluorescent proteins, focusing on the contributions provided by pioneering work from the lab of the late Professor Chris Hawes.
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Affiliation(s)
- V Kriechbaumer
- Plant Cell Biology, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, U.K
| | - F Brandizzi
- MSU-DOE Plant Research Laboratory, Department of Plant Biology, Michigan State University, East Lansing, Michigan, U.S.A
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25
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Gonçalves CS, Le Boiteux E, Arnaud P, Costa BM. HOX gene cluster (de)regulation in brain: from neurodevelopment to malignant glial tumours. Cell Mol Life Sci 2020; 77:3797-3821. [PMID: 32239260 PMCID: PMC11105007 DOI: 10.1007/s00018-020-03508-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/10/2020] [Accepted: 03/17/2020] [Indexed: 12/19/2022]
Abstract
HOX genes encode a family of evolutionarily conserved homeodomain transcription factors that are crucial both during development and adult life. In humans, 39 HOX genes are arranged in four clusters (HOXA, B, C, and D) in chromosomes 7, 17, 12, and 2, respectively. During embryonic development, particular epigenetic states accompany their expression along the anterior-posterior body axis. This tightly regulated temporal-spatial expression pattern reflects their relative chromosomal localization, and is critical for normal embryonic brain development when HOX genes are mainly expressed in the hindbrain and mostly absent in the forebrain region. Epigenetic marks, mostly polycomb-associated, are dynamically regulated at HOX loci and regulatory regions to ensure the finely tuned HOX activation and repression, highlighting a crucial epigenetic plasticity necessary for homeostatic development. HOX genes are essentially absent in healthy adult brain, whereas they are detected in malignant brain tumours, namely gliomas, where HOX genes display critical roles by regulating several hallmarks of cancer. Here, we review the major mechanisms involved in HOX genes (de)regulation in the brain, from embryonic to adult stages, in physiological and oncologic conditions. We focus particularly on the emerging causes of HOX gene deregulation in glioma, as well as on their functional and clinical implications.
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Affiliation(s)
- Céline S Gonçalves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Elisa Le Boiteux
- Université Clermont Auvergne, CNRS, INSERM-iGReD, Clermont-Ferrand, France
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, INSERM-iGReD, Clermont-Ferrand, France
| | - Bruno M Costa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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26
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Lewis EMA, Sankar S, Tong C, Patterson ES, Waller LE, Gontarz P, Zhang B, Ornitz DM, Kroll KL. Geminin is required for Hox gene regulation to pattern the developing limb. Dev Biol 2020; 464:11-23. [PMID: 32450229 DOI: 10.1016/j.ydbio.2020.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/09/2020] [Accepted: 05/13/2020] [Indexed: 02/07/2023]
Abstract
Development of the complex structure of the vertebrate limb requires carefully orchestrated interactions between multiple regulatory pathways and proteins. Among these, precise regulation of 5' Hox transcription factor expression is essential for proper limb bud patterning and elaboration of distinct limb skeletal elements. Here, we identified Geminin (Gmnn) as a novel regulator of this process. A conditional model of Gmnn deficiency resulted in loss or severe reduction of forelimb skeletal elements, while both the forelimb autopod and hindlimb were unaffected. 5' Hox gene expression expanded into more proximal and anterior regions of the embryonic forelimb buds in this Gmnn-deficient model. A second conditional model of Gmnn deficiency instead caused a similar but less severe reduction of hindlimb skeletal elements and hindlimb polydactyly, while not affecting the forelimb. An ectopic posterior SHH signaling center was evident in the anterior hindlimb bud of Gmnn-deficient embryos in this model. This center ectopically expressed Hoxd13, the HOXD13 target Shh, and the SHH target Ptch1, while these mutant hindlimb buds also had reduced levels of the cleaved, repressor form of GLI3, a SHH pathway antagonist. Together, this work delineates a new role for Gmnn in modulating Hox expression to pattern the vertebrate limb.
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Affiliation(s)
- Emily M A Lewis
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Savita Sankar
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Caili Tong
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ethan S Patterson
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Laura E Waller
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Paul Gontarz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Bo Zhang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David M Ornitz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kristen L Kroll
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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27
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HOX13-dependent chromatin accessibility underlies the transition towards the digit development program. Nat Commun 2020; 11:2491. [PMID: 32427842 PMCID: PMC7237422 DOI: 10.1038/s41467-020-16317-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/20/2020] [Indexed: 12/05/2022] Open
Abstract
Hox genes encode transcription factors (TFs) that establish morphological diversity in the developing embryo. The similar DNA-binding motifs of the various HOX TFs contrast with the wide-range of HOX-dependent genetic programs. The influence of the chromatin context on HOX binding specificity remains elusive. Here, we used the developing limb as a model system to compare the binding specificity of HOXA13 and HOXD13 (HOX13 hereafter), which are required for digit formation, and HOXA11, involved in forearm/leg development. We find that upon ectopic expression in distal limb buds, HOXA11 binds sites normally HOX13-specific. Importantly, these sites are loci whose chromatin accessibility relies on HOX13. Moreover, we show that chromatin accessibility specific to the distal limb requires HOX13 function. Based on these results, we propose that HOX13 TFs pioneer the distal limb-specific chromatin accessibility landscape for the proper implementation of the distal limb developmental program. Pioneer factors direct cell fate through switching inaccessible chromatin to an accessible state at specific target enhancers. Here the authors show that HOX13 transcription factors have a pioneer activity which is required for the proper implementation of the distal limb developmental program.
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28
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Miller SW, Posakony JW. Disparate expression specificities coded by a shared Hox-C enhancer. eLife 2020; 9:39876. [PMID: 32342858 PMCID: PMC7188484 DOI: 10.7554/elife.39876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
Can a single regulatory sequence be shared by two genes undergoing functional divergence? Here we describe a single promiscuous enhancer within the Drosophila Antennapedia Complex, EO053, that directs aspects of the expression of two adjacent genes, pb (a Hox2 ortholog) and zen2 (a divergent Hox3 paralog), with disparate spatial and temporal expression patterns. We were unable to separate the pb-like and zen2-like specificities within EO053, and we identify sequences affecting both expression patterns. Importantly, genomic deletion experiments demonstrate that EO053 cooperates with additional pb- and zen2-specific enhancers to regulate the mRNA expression of both genes. We examine sequence conservation of EO053 within the Schizophora, and show that patterns of synteny between the Hox2 and Hox3 orthologs in Arthropods are consistent with a shared regulatory relationship extending prior to the Hox3/zen divergence. Thus, EO053 represents an example of two genes having evolved disparate outputs while utilizing this shared regulatory region. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Steve W Miller
- Division of Biological Sciences, Section of Cell & Developmental Biology, University of California San Diego, La Jolla, United States
| | - James W Posakony
- Division of Biological Sciences, Section of Cell & Developmental Biology, University of California San Diego, La Jolla, United States
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29
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Amândio AR, Lopez-Delisle L, Bolt CC, Mascrez B, Duboule D. A complex regulatory landscape involved in the development of mammalian external genitals. eLife 2020; 9:e52962. [PMID: 32301703 PMCID: PMC7185996 DOI: 10.7554/elife.52962] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 04/17/2020] [Indexed: 02/04/2023] Open
Abstract
Developmental genes are often controlled by large regulatory landscapes matching topologically associating domains (TADs). In various contexts, the associated chromatin backbone is modified by specific enhancer-enhancer and enhancer-promoter interactions. We used a TAD flanking the mouse HoxD cluster to study how these regulatory architectures are formed and deconstructed once their function achieved. We describe this TAD as a functional unit, with several regulatory sequences acting together to elicit a transcriptional response. With one exception, deletion of these sequences didn't modify the transcriptional outcome, a result at odds with a conventional view of enhancer function. The deletion and inversion of a CTCF site located near these regulatory sequences did not affect transcription of the target gene. Slight modifications were nevertheless observed, in agreement with the loop extrusion model. We discuss these unexpected results considering both conventional and alternative explanations relying on the accumulation of poorly specific factors within the TAD backbone.
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Affiliation(s)
- Ana Rita Amândio
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Christopher Chase Bolt
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of GenevaGenevaSwitzerland
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- Department of Genetics and Evolution, University of GenevaGenevaSwitzerland
- Collège de FranceParisFrance
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30
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Abstract
Regulatory landscapes have been defined in vertebrates as large DNA segments containing diverse enhancer sequences that produce coherent gene transcription. These genomic platforms integrate multiple cellular signals and hence can trigger pleiotropic expression of developmental genes. Identifying and evaluating how these chromatin regions operate may be difficult as the underlying regulatory mechanisms can be as unique as the genes they control. In this brief article and accompanying poster, we discuss some of the ways in which regulatory landscapes operate, illustrating these mechanisms using genes important for vertebrate development as examples. We also highlight some of the techniques available to researchers for analysing regulatory landscapes.
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Affiliation(s)
- Christopher Chase Bolt
- Swiss Institute for Cancer Research (ISREC), School of Life Sciences, Federal Institute of Technology, Lausanne, 1015 Lausanne, Switzerland
| | - Denis Duboule
- Swiss Institute for Cancer Research (ISREC), School of Life Sciences, Federal Institute of Technology, Lausanne, 1015 Lausanne, Switzerland
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
- Collège de France, 75005 Paris, France
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31
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Williams RM, Candido-Ferreira I, Repapi E, Gavriouchkina D, Senanayake U, Ling ITC, Telenius J, Taylor S, Hughes J, Sauka-Spengler T. Reconstruction of the Global Neural Crest Gene Regulatory Network In Vivo. Dev Cell 2019; 51:255-276.e7. [PMID: 31639368 PMCID: PMC6838682 DOI: 10.1016/j.devcel.2019.10.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 05/31/2019] [Accepted: 10/01/2019] [Indexed: 02/07/2023]
Abstract
Precise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and dynamic molecular interactions. Here we present a genome-wide in vivo reconstruction of the GRN underlying development of the multipotent neural crest (NC) embryonic cell population. By coupling NC-specific epigenomic and transcriptional profiling at population and single-cell levels with genome/epigenome engineering in vivo, we identify multiple regulatory layers governing NC ontogeny, including NC-specific enhancers and super-enhancers, novel trans-factors, and cis-signatures allowing reverse engineering of the NC-GRN at unprecedented resolution. Furthermore, identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene circuits that define canonical and neural NC fates early during NC ontogeny. Our integrated approach, allowing dissection of cell-type-specific regulatory circuits in vivo, has broad implications for GRN discovery and investigation.
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Affiliation(s)
- Ruth M Williams
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Ivan Candido-Ferreira
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Emmanouela Repapi
- University of Oxford, MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - Daria Gavriouchkina
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Upeka Senanayake
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Irving T C Ling
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK; University of Oxford, Department of Paediatric Surgery, Children's Hospital Oxford, Oxford, UK
| | - Jelena Telenius
- University of Oxford, MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK; University of Oxford, MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Stephen Taylor
- University of Oxford, MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - Jim Hughes
- University of Oxford, MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK; University of Oxford, MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK.
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32
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Le Caignec C, Pichon O, Briand A, de Courtivron B, Bonnard C, Lindenbaum P, Redon R, Schluth-Bolard C, Diguet F, Rollat-Farnier PA, Sanchez-Castro M, Vuillaume ML, Sanlaville D, Duboule D, Mégarbané A, Toutain A. Fryns type mesomelic dysplasia of the upper limbs caused by inverted duplications of the HOXD gene cluster. Eur J Hum Genet 2019; 28:324-332. [PMID: 31591517 DOI: 10.1038/s41431-019-0522-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 07/12/2019] [Accepted: 09/17/2019] [Indexed: 01/09/2023] Open
Abstract
The HoxD cluster is critical for vertebrate limb development. Enhancers located in both the telomeric and centromeric gene deserts flanking the cluster regulate the transcription of HoxD genes. In rare patients, duplications, balanced translocations or inversions misregulating HOXD genes are responsible for mesomelic dysplasia of the upper and lower limbs. By aCGH, whole-genome mate-pair sequencing, long-range PCR and fiber fluorescent in situ hybridization, we studied patients from two families displaying mesomelic dysplasia limited to the upper limbs. We identified microduplications including the HOXD cluster and showed that microduplications were in an inverted orientation and inserted between the HOXD cluster and the telomeric enhancers. Our results highlight the existence of an autosomal dominant condition consisting of isolated ulnar dysplasia caused by microduplications inserted between the HOXD cluster and the telomeric enhancers. The duplications likely disconnect the HOXD9 to HOXD11 genes from their regulatory sequences. This presumptive loss-of-function may have contributed to the phenotype. In both cases, however, these rearrangements brought HOXD13 closer to telomeric enhancers, suggesting that the alterations derive from the dominant-negative effect of this digit-specific protein when ectopically expressed during the early development of forearms, through the disruption of topologically associating domain structure at the HOXD locus.
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Affiliation(s)
- Cédric Le Caignec
- CHU Nantes, Service de Génétique Médicale, Nantes, France. .,Universite de Nantes, Nantes, France.
| | - Olivier Pichon
- CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Annaig Briand
- CHU Nantes, Service de Génétique Médicale, Nantes, France
| | | | - Christian Bonnard
- Service de Chirurgie Orthopédique Pédiatrique, CHRU de Tours, Tours, France.,Université François-Rabelais de Tours, PRES Centre-Val de Loire Université, Tours, France
| | - Pierre Lindenbaum
- INSERM, UMR_S1087, l'institut du thorax, Nantes, France.,CNRS, UMR 6291, Nantes, France
| | - Richard Redon
- INSERM, UMR_S1087, l'institut du thorax, Nantes, France.,CNRS, UMR 6291, Nantes, France
| | - Caroline Schluth-Bolard
- Department of Genetics, Lyon University Hospital, Lyon, France.,Claude Bernard Lyon I University, Lyon, France.,CRNL, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - Flavie Diguet
- Department of Genetics, Lyon University Hospital, Lyon, France
| | | | | | - Marie-Laure Vuillaume
- Service de Génétique, Hôpital Bretonneau, CHU, Tours, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - Damien Sanlaville
- Department of Genetics, Lyon University Hospital, Lyon, France.,Claude Bernard Lyon I University, Lyon, France.,CRNL, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - Denis Duboule
- University of Geneva and Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | | | - Annick Toutain
- Service de Génétique, Hôpital Bretonneau, CHU, Tours, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
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33
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Rodríguez-Carballo E, Lopez-Delisle L, Yakushiji-Kaminatsui N, Ullate-Agote A, Duboule D. Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes. BMC Biol 2019; 17:55. [PMID: 31299961 PMCID: PMC6626364 DOI: 10.1186/s12915-019-0677-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/28/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The spatial organization of the mammalian genome relies upon the formation of chromatin domains of various scales. At the level of gene regulation in cis, collections of enhancer sequences define large regulatory landscapes that usually match with the presence of topologically associating domains (TADs). These domains often contain ranges of enhancers displaying similar or related tissue specificity, suggesting that in some cases, such domains may act as coherent regulatory units, with a global on or off state. By using the HoxD gene cluster, which specifies the topology of the developing limbs via highly orchestrated regulation of gene expression, as a paradigm, we investigated how the arrangement of regulatory domains determines their activity and function. RESULTS Proximal and distal cells in the developing limb express different levels of Hoxd genes, regulated by flanking 3' and 5' TADs, respectively. We characterized the effect of large genomic rearrangements affecting these two TADs, including their fusion into a single chromatin domain. We show that, within a single hybrid TAD, the activation of both proximal and distal limb enhancers globally occurred as when both TADs are intact. However, the activity of the 3' TAD in distal cells is generally increased in the fused TAD, when compared to wild type where it is silenced. Also, target gene activity in distal cells depends on whether or not these genes had previously responded to proximal enhancers, which determines the presence or absence of H3K27me3 marks. We also show that the polycomb repressive complex 2 is mainly recruited at the Hox gene cluster and can extend its coverage to far-cis regulatory sequences as long as confined to the neighboring TAD structure. CONCLUSIONS We conclude that antagonistic limb proximal and distal enhancers can exert their specific effects when positioned into the same TAD and in the absence of their genuine target genes. We also conclude that removing these target genes reduced the coverage of a regulatory landscape by chromatin marks associated with silencing, which correlates with its prolonged activity in time.
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Affiliation(s)
- Eddie Rodríguez-Carballo
- Laboratory of Developmental Genomics, Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland
| | - Lucille Lopez-Delisle
- School of Life Sciences, Federal Institute of Technology, Lausanne, 1015, Lausanne, Switzerland
| | - Nayuta Yakushiji-Kaminatsui
- School of Life Sciences, Federal Institute of Technology, Lausanne, 1015, Lausanne, Switzerland
- Present Address: Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohoma, Kanagawa, 230-0045, Japan
| | - Asier Ullate-Agote
- Laboratory of Artificial and Natural Evolution, Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland
| | - Denis Duboule
- Laboratory of Developmental Genomics, Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland.
- School of Life Sciences, Federal Institute of Technology, Lausanne, 1015, Lausanne, Switzerland.
- Collège de France, 75005, Paris, France.
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Gentile C, Berlivet S, Mayran A, Paquette D, Guerard-Millet F, Bajon E, Dostie J, Kmita M. PRC2-Associated Chromatin Contacts in the Developing Limb Reveal a Possible Mechanism for the Atypical Role of PRC2 in HoxA Gene Expression. Dev Cell 2019; 50:184-196.e4. [DOI: 10.1016/j.devcel.2019.05.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 03/24/2019] [Accepted: 05/09/2019] [Indexed: 10/26/2022]
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Xiao J, Yang SS, Wu JX, Wang H, Yu X, Shang W, Chen GQ, Gu ZY. Highly Selective Capture of Monophosphopeptides by Two-Dimensional Metal–Organic Framework Nanosheets. Anal Chem 2019; 91:9093-9101. [DOI: 10.1021/acs.analchem.9b01581] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jing Xiao
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Shi-Shu Yang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Jian-Xiang Wu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - He Wang
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Avenue, Nanjing, 210061, China
| | - Xizhong Yu
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wenbin Shang
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Gui-Quan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Avenue, Nanjing, 210061, China
| | - Zhi-Yuan Gu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
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Sanese P, Forte G, Disciglio V, Grossi V, Simone C. FOXO3 on the Road to Longevity: Lessons From SNPs and Chromatin Hubs. Comput Struct Biotechnol J 2019; 17:737-745. [PMID: 31303978 PMCID: PMC6606898 DOI: 10.1016/j.csbj.2019.06.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/31/2019] [Accepted: 06/11/2019] [Indexed: 12/21/2022] Open
Abstract
Health span is driven by a precise interplay between genes and the environment. Cell response to environmental cues is mediated by signaling cascades and genetic variants that affect gene expression by regulating chromatin plasticity. Indeed, they can promote the interaction of promoters with regulatory elements by forming active chromatin hubs. FOXO3 encodes a transcription factor with a strong impact on aging and age-related phenotypes, as it regulates stress response, therefore affecting lifespan. A significant association has been shown between human longevity and several FOXO3 variants located in intron 2. This haplotype block forms a putative aging chromatin hub in which FOXO3 has a central role, as it modulates the physical connection and activity of neighboring genes involved in age-related processes. Here we describe the role of FOXO3 and its single-nucleotide polymorphisms (SNPs) in healthy aging, with a focus on the enhancer region encompassing the SNP rs2802292, which upregulates FOXO3 expression and can promote the activity of the aging hub in response to different stress stimuli. FOXO3 protective effect on lifespan may be due to the accessibility of this region to transcription factors promoting its expression. This could in part explain the differences in FOXO3 association with longevity between genders, as its activity in females may be modulated by estrogens through estrogen receptor response elements located in the rs2802292-encompassing region. Altogether, the molecular mechanisms described here may help establish whether the rs2802292 SNP can be taken advantage of in predictive medicine and define the potential of targeting FOXO3 for age-related diseases.
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Key Words
- 3C, Chromosome conformation capture
- 5′UTR, Five prime untranslated region
- ACH, Active chromatin hub
- Aging
- Chromatin hub
- ER, Estrogen receptor
- ERE, Estrogen-responsive element
- FHRE, Forkhead response element
- FOXO3
- FOXO3, Forkhead box 3
- GPx, Glutathione peroxidase
- GWAS, Genome-wide association study
- HPS, Hamartomatous polyposis syndrome
- HSE, Heat shock element
- HSF1, Heat shock factor 1
- IGF-1, Insulin growth factor-1
- LD, Linkage disequilibrium
- Longevity
- PHTS, PTEN hamartoma tumor syndrome
- PJS, Peutz-Jeghers syndrome
- ROS, Reactive oxygen species
- SNP
- SNP, Single nucleotide polymorphism
- SNV, Single nucleotide variant
- SOD2, Superoxide dismutase 2
- TAD, Topologically associated domain
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Affiliation(s)
- Paola Sanese
- Medical Genetics, Department of Biomedical Sciences and Human Oncology (DIMO), University of Bari Aldo Moro, Piazza G. Cesare, 11, 70124 Bari, Italy
| | - Giovanna Forte
- Medical Genetics, National Institute of Gastroenterology 'S. de Bellis' Research Hospital, Via Turi, 27, 70013 Castellana Grotte (BA), Italy
| | - Vittoria Disciglio
- Medical Genetics, National Institute of Gastroenterology 'S. de Bellis' Research Hospital, Via Turi, 27, 70013 Castellana Grotte (BA), Italy
| | - Valentina Grossi
- Medical Genetics, National Institute of Gastroenterology 'S. de Bellis' Research Hospital, Via Turi, 27, 70013 Castellana Grotte (BA), Italy
| | - Cristiano Simone
- Medical Genetics, Department of Biomedical Sciences and Human Oncology (DIMO), University of Bari Aldo Moro, Piazza G. Cesare, 11, 70124 Bari, Italy.,Medical Genetics, National Institute of Gastroenterology 'S. de Bellis' Research Hospital, Via Turi, 27, 70013 Castellana Grotte (BA), Italy
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Onimaru K, Kuraku S. Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications. Brief Funct Genomics 2019; 17:352-361. [PMID: 29566222 PMCID: PMC6158797 DOI: 10.1093/bfgp/ely008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Inferring the phenotype of the last common ancestor of living vertebrates is a challenging problem because of several unresolvable factors. They include the lack of reliable out-groups of living vertebrates, poor information about less fossilizable organs and specialized traits of phylogenetically important species, such as lampreys and hagfishes (e.g. secondary loss of vertebrae in adult hagfishes). These factors undermine the reliability of ancestral reconstruction by traditional character mapping approaches based on maximum parsimony. In this article, we formulate an approach to hypothesizing ancestral vertebrate phenotypes using information from the phylogenetic and functional properties of genes duplicated by genome expansions in early vertebrate evolution. We named the conjecture as ‘chronological reconstruction of ohnolog functions (CHROF)’. This CHROF conjecture raises the possibility that the last common ancestor of living vertebrates may have had more complex traits than currently thought.
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Affiliation(s)
- Koh Onimaru
- RIKEN Center for Life Science Technologies, Kobe, Hyogo Japan.,Department of biological science, Tokyo Institute of Technology, Tokyo, Japan
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38
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Fabre PJ, Leleu M, Mascrez B, Lo Giudice Q, Cobb J, Duboule D. Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development. BMC Biol 2018; 16:101. [PMID: 30223853 PMCID: PMC6142630 DOI: 10.1186/s12915-018-0570-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/29/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Global analyses of gene expression during development reveal specific transcription patterns associated with the emergence of various cell types, tissues, and organs. These heterogeneous patterns are instrumental to ensure the proper formation of the different parts of our body, as shown by the phenotypic effects generated by functional genetic approaches. However, variations at the cellular level can be observed within each structure or organ. In the developing mammalian limbs, expression of Hox genes from the HoxD cluster is differentially controlled in space and time, in cells that will pattern the digits and the forearms. While the Hoxd genes broadly share a common regulatory landscape and large-scale analyses have suggested a homogenous Hox gene transcriptional program, it has not previously been clear whether Hoxd genes are expressed together at the same levels in the same cells. RESULTS We report a high degree of heterogeneity in the expression of the Hoxd11 and Hoxd13 genes. We analyzed single-limb bud cell transcriptomes and show that Hox genes are expressed in specific combinations that appear to match particular cell types. In cells giving rise to digits, we find that the expression of the five relevant Hoxd genes (Hoxd9 to Hoxd13) is unbalanced, despite their control by known global enhancers. We also report that specific combinatorial expression follows a pseudo-time sequence, which is established based on the transcriptional diversity of limb progenitors. CONCLUSIONS Our observations reveal the existence of distinct combinations of Hoxd genes at the single-cell level during limb development. In addition, we document that the increasing combinatorial expression of Hoxd genes in this developing structure is associated with specific transcriptional signatures and that these signatures illustrate a temporal progression in the differentiation of these cells.
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Affiliation(s)
- P J Fabre
- School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, 1015, Lausanne, Switzerland. .,Department of Basic Neurosciences, University of Geneva, 1211, Geneva, Switzerland.
| | - M Leleu
- School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, 1015, Lausanne, Switzerland
| | - B Mascrez
- Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland
| | - Q Lo Giudice
- Department of Basic Neurosciences, University of Geneva, 1211, Geneva, Switzerland
| | - J Cobb
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - D Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, 1015, Lausanne, Switzerland. .,Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland.
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Durston AJ. Two Tier Hox Collinearity Mediates Vertebrate Axial Patterning. Front Cell Dev Biol 2018; 6:102. [PMID: 30234110 PMCID: PMC6131192 DOI: 10.3389/fcell.2018.00102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/10/2018] [Indexed: 12/04/2022] Open
Abstract
A two tier mechanism mediates Hox collinearity. Besides the familiar collinear chromatin modification within each Hox cluster (nanocollinearity), there is also a macrocollinearity tier. Individual Hox clusters and individual cells are coordinated and synchronized to generate multiscale (macro and nano) collinearity in the early vertebrate embryo. Macro-collinearity is mediated by three non-cell autonomous Hox–Hox interactions. These mediate temporal collinearity in early NOM (non-organizer mesoderm), time space translation where temporal collinearity is translated to spatial collinearity along the early embryo’s main body axis and neural transformation, where Hox expression is copied monospecifically from NOM mesoderm to overlying neurectoderm in the late gastrula. Unlike nanocollinearity, which is Hox cluster restricted, axial macrocollinearity extends into the head and EAD domains, thus covering the whole embryonic anterior-posterior (A-P) axis. EAD: extreme anterior domain, the only A-P axial domain anterior to the head. The whole time space translation mechanism interacts with A-P signaling pathways via “decision points,” separating different domains on the axis.
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Affiliation(s)
- Antony J Durston
- Faculty of Science, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
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40
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Sun Y, Dai H, Chen S, Zhang Y, Wu T, Cao X, Zhao G, Xu A, Wang J, Wu L. Disruption of Chromosomal Architecture of cox2 Locus Sensitizes Lung Cancer Cells to Radiotherapy. Mol Ther 2018; 26:2456-2465. [PMID: 30131302 PMCID: PMC6171098 DOI: 10.1016/j.ymthe.2018.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/27/2018] [Accepted: 08/01/2018] [Indexed: 11/15/2022] Open
Abstract
Despite treatment of lung cancer with radiotherapy and chemotherapy, the survival rate of lung cancer patients remains poor. Previous studies demonstrated the importance of upregulation of inflammatory factors, such as cyclooxygenase 2 (cox2), in tumor tolerance. In the present study, we investigated the role of cox2 in radiosensitivity of lung cancer. Our results showed that the combination treatment of radiation with aspirin, an anti-inflammatory drug, induced a synergistic reduction of cell survival in A549 and H1299 lung cancer cells. In comparison with normal human lung fibroblasts (NHLFs), the cell viability was significantly decreased and the level of apoptosis was remarkably enhanced in A549 cells. Mechanistic studies revealed that the reduction of cox2 by aspirin in A549 and H1299 was caused by disruption of the chromosomal architecture of the cox2 locus. Moreover, the disruption of chromatin looping was mediated by the inhibition of nuclear translocation of p65 and decreased enrichment of p65 at cox2-regulatory elements. Importantly, disorganization of the chromosomal architecture of cox2 triggered A549 cells sensitive to γ-radiation by the induction of apoptosis. In conclusion, we present evidence of an effective therapeutic treatment targeting the epigenetic regulation of lung cancer and a potential strategy to overcome radiation resistance in cancer cells.
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Affiliation(s)
- Yuxiang Sun
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China
| | - Hui Dai
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China
| | - Shaopeng Chen
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China.
| | - Yajun Zhang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China
| | - Tao Wu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China
| | - Xianbin Cao
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China
| | - Guoping Zhao
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China
| | - An Xu
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China
| | - Jun Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China
| | - Lijun Wu
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China.
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Breuss MW, Nguyen A, Song Q, Nguyen T, Stanley V, James KN, Musaev D, Chai G, Wirth SA, Anzenberg P, George RD, Johansen A, Ali S, Zia-Ur-Rehman M, Sultan T, Zaki MS, Gleeson JG. Mutations in LNPK, Encoding the Endoplasmic Reticulum Junction Stabilizer Lunapark, Cause a Recessive Neurodevelopmental Syndrome. Am J Hum Genet 2018; 103:296-304. [PMID: 30032983 PMCID: PMC6080764 DOI: 10.1016/j.ajhg.2018.06.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/27/2018] [Indexed: 11/16/2022] Open
Abstract
The dynamic shape of the endoplasmic reticulum (ER) is a reflection of its wide variety of critical cell biological functions. Consequently, perturbation of ER-shaping proteins can cause a range of human phenotypes. Here, we describe three affected children (from two consanguineous families) who carry homozygous loss-of-function mutations in LNPK (previously known as KIAA1715); this gene encodes lunapark, which is proposed to serve as a curvature-stabilizing protein within tubular three-way junctions of the ER. All individuals presented with severe psychomotor delay, intellectual disability, hypotonia, epilepsy, and corpus callosum hypoplasia, and two of three showed mild cerebellar hypoplasia and atrophy. Consistent with a proposed role in neurodevelopmental disease, LNPK was expressed during brain development in humans and mice and was present in neurite-like processes in differentiating human neural progenitor cells. Affected cells showed the absence of full-length lunapark, aberrant ER structures, and increased luminal mass density. Together, our results implicate the ER junction stabilizer lunapark in establishing the corpus callosum.
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Affiliation(s)
- Martin W Breuss
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - An Nguyen
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Qiong Song
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Thai Nguyen
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Valentina Stanley
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Kiely N James
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Damir Musaev
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Guoliang Chai
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Sara A Wirth
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Paula Anzenberg
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Renee D George
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Anide Johansen
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Shaila Ali
- Department of Pediatric Neurology, Children's Hospital and Institute of Child Health, Lahore 54000, Pakistan
| | - Muhammad Zia-Ur-Rehman
- Department of Pediatric Neurology, Children's Hospital and Institute of Child Health, Lahore 54000, Pakistan
| | - Tipu Sultan
- Department of Pediatric Neurology, Children's Hospital and Institute of Child Health, Lahore 54000, Pakistan
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12311, Egypt
| | - Joseph G Gleeson
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA.
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Chen S, Cui Y, Parashar S, Novick PJ, Ferro-Novick S. ER-phagy requires Lnp1, a protein that stabilizes rearrangements of the ER network. Proc Natl Acad Sci U S A 2018; 115:E6237-E6244. [PMID: 29915089 PMCID: PMC6142256 DOI: 10.1073/pnas.1805032115] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The endoplasmic reticulum (ER) forms a contiguous network of tubules and sheets that is predominantly associated with the cell cortex in yeast. Upon treatment with rapamycin, the ER undergoes degradation by selective autophagy. This process, termed ER-phagy, requires Atg40, a selective autophagy receptor that localizes to the cortical ER. Here we report that ER-phagy also requires Lnp1, an ER membrane protein that normally resides at the three-way junctions of the ER network, where it serves to stabilize the network as it is continually remodeled. Rapamycin treatment increases the expression of Atg40, driving ER domains marked by Atg40 puncta to associate with Atg11, a scaffold protein needed to form autophagosomes. Although Atg40 largely localizes to the cortical ER, the autophagy machinery resides in the cell interior. The localization of Atg40 to sites of autophagosome formation is blocked in an lnp1Δ mutant or upon treatment of wild-type cells with the actin-depolymerizing drug Latrunculin A. This prevents the association of Atg40 with Atg11 and the packaging of the ER into autophagosomes. We propose that Lnp1 is needed to stabilize the actin-dependent remodeling of the ER that is essential for ER-phagy.
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Affiliation(s)
- Shuliang Chen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0668
| | - Yixian Cui
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0668
| | - Smriti Parashar
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0668
| | - Peter J Novick
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0668
| | - Susan Ferro-Novick
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0668
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Izzi B, Noro F, Cludts K, Freson K, Hoylaerts MF. Cell-Specific PEAR1 Methylation Studies Reveal a Locus that Coordinates Expression of Multiple Genes. Int J Mol Sci 2018; 19:ijms19041069. [PMID: 29614055 PMCID: PMC5979289 DOI: 10.3390/ijms19041069] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/19/2018] [Accepted: 03/28/2018] [Indexed: 02/07/2023] Open
Abstract
Chromosomal interactions connect distant enhancers and promoters on the same chromosome, activating or repressing gene expression. PEAR1 encodes the Platelet-Endothelial Aggregation Receptor 1, a contact receptor involved in platelet function and megakaryocyte and endothelial cell proliferation. PEAR1 expression during megakaryocyte differentiation is controlled by DNA methylation at its first CpG island. We identified a PEAR1 cell-specific methylation sensitive region in endothelial cells and megakaryocytes that showed strong chromosomal interactions with ISGL20L2, RRNAD1, MRLP24, HDGF and PRCC, using available promoter capture Hi-C datasets. These genes are involved in ribosome processing, protein synthesis, cell cycle and cell proliferation. We next studied the methylation and expression profile of these five genes in Human Umbilical Vein Endothelial Cells (HUVECs) and megakaryocyte precursors. While cell-specific PEAR1 methylation corresponded to variability in expression for four out of five genes, no methylation change was observed in their promoter regions across cell types. Our data suggest that PEAR1 cell-type specific methylation changes may control long distance interactions with other genes. Further studies are needed to show whether such interaction data might be relevant for the genome-wide association data that showed a role for non-coding PEAR1 variants in the same region and platelet function, platelet count and cardiovascular risk.
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Affiliation(s)
- Benedetta Izzi
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, 3000 Leuven, Belgium.
| | - Fabrizia Noro
- Department of Epidemiology and Prevention, IRCCS Istituto Neurologico Mediterraneo Neuromed, Via dell'Elettronica, 86077 Pozzilli (IS), Italy.
| | - Katrien Cludts
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, 3000 Leuven, Belgium.
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, 3000 Leuven, Belgium.
| | - Marc F Hoylaerts
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, 3000 Leuven, Belgium.
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44
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Catarino RR, Stark A. Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation. Genes Dev 2018; 32:202-223. [PMID: 29491135 PMCID: PMC5859963 DOI: 10.1101/gad.310367.117] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Enhancers are important genomic regulatory elements directing cell type-specific transcription. They assume a key role during development and disease, and their identification and functional characterization have long been the focus of scientific interest. The advent of next-generation sequencing and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-based genome editing has revolutionized the means by which we study enhancer biology. In this review, we cover recent developments in the prediction of enhancers based on chromatin characteristics and their identification by functional reporter assays and endogenous DNA perturbations. We discuss that the two latter approaches provide different and complementary insights, especially in assessing enhancer sufficiency and necessity for transcription activation. Furthermore, we discuss recent insights into mechanistic aspects of enhancer function, including findings about cofactor requirements and the role of post-translational histone modifications such as monomethylation of histone H3 Lys4 (H3K4me1). Finally, we survey how these approaches advance our understanding of transcription regulation with respect to promoter specificity and transcriptional bursting and provide an outlook covering open questions and promising developments.
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Affiliation(s)
- Rui R Catarino
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
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45
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Chong A, Teo JX, Ban KHK. Distinct epigenetic signatures elucidate enhancer-gene relationships that delineate CIMP and non-CIMP colorectal cancers. Oncotarget 2018; 7:28027-39. [PMID: 27049830 PMCID: PMC5053707 DOI: 10.18632/oncotarget.8473] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/14/2016] [Indexed: 12/22/2022] Open
Abstract
Epigenetic changes, like DNA methylation, affect gene expression and in colorectal cancer (CRC), a distinct phenotype called the CpG island methylator phenotype (“CIMP”) has significantly higher levels of DNA methylation at so-called “Type C loci” within the genome. We postulate that enhancer-gene pairs are coordinately controlled through DNA methylation in order to regulate the expression of key genes/biomarkers for a particular phenotype. Firstly, we found 24 experimentally-validated enhancers (VISTA enhancer browser) that contained statistically significant (FDR-adjusted q-value of <0.01) differentially methylated regions (DMRs) (1000bp) in a study of CIMP versus non-CIMP CRCs. Of these, the methylation of 2 enhancers, 1702 and 1944, were found to be very well correlated with the methylation of the genes Wnt3A and IGDCC3, respectively, in two separate and independent datasets. We show for the first time that there are indeed distinct and dynamic changes in the methylation pattern of specific enhancer-gene pairs in CRCs. Such a coordinated epigenetic event could be indicative of an interaction between (1) enhancer 1702 and Wnt3A and (2) enhancer 1944 and IGDCC3. Moreover, our study shows that the methylation patterns of these 2 enhancer-gene pairs can potentially be used as biomarkers to delineate CIMP from non-CIMP CRCs.
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Affiliation(s)
- Allen Chong
- Department of Pathology, National University of Singapore, 119074 Singapore.,Present address: Shanxi Guoxin Caregeno Medical Laboratories, Taiyuan, Shanxi Province, 030006 China
| | - Jing Xian Teo
- Cancer Science Institute, National University of Singapore, 117599 Singapore
| | - Kenneth H K Ban
- Department of Biochemistry, National University of Singapore, 117596 Singapore.,Institute of Molecular and Cell Biology, 138673 Singapore
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46
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Deletion of a Long-Range Dlx5 Enhancer Disrupts Inner Ear Development in Mice. Genetics 2018; 208:1165-1179. [PMID: 29301908 DOI: 10.1534/genetics.117.300447] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/09/2017] [Indexed: 12/19/2022] Open
Abstract
Distal enhancers are thought to play important roles in the spatiotemporal regulation of gene expression during embryonic development, but few predicted enhancer elements have been shown to affect transcription of their endogenous genes or to alter phenotypes when disrupted. Here, we demonstrate that a 123.6-kb deletion within the mouse Slc25a13 gene is associated with reduced transcription of Dlx5, a gene located 660 kb away. Mice homozygous for the Slc25a13 deletion mutation [named hyperspin (hspn)] have malformed inner ears and are deaf with balance defects, whereas previously reported Slc25a13 knockout mice showed no phenotypic abnormalities. Inner ears of Slc25a13hspn/hspn mice have malformations similar to those of Dlx5-/- embryos, and Dlx5 expression is severely reduced in the otocyst but not the branchial arches of Slc25a13hspn/hspn embryos, indicating that the Slc25a13hspn deletion affects otic-specific enhancers of Dlx5 In addition, transheterozygous Slc25a13+/hspn Dlx5+/- mice exhibit noncomplementation with inner ear dysmorphologies similar to those of Slc25a13hspn/hspn and Dlx5-/-embryos, verifying a cis-acting effect of the Slc25a13hspn deletion on Dlx5 expression. CRISPR/Cas9-mediated deletions of putative enhancer elements located within the Slc25a13hspn deleted region failed to phenocopy the defects of Slc25a13hspn/hspn mice, suggesting the possibility of multiple enhancers with redundant functions. Our findings in mice suggest that analogous enhancer elements in the human SLC25A13 gene may regulate DLX5 expression and underlie the hearing loss that is associated with split-hand/-foot malformation 1 syndrome. Slc25a13hspn/hspn mice provide a new animal model for studying long-range enhancer effects on Dlx5 expression in the developing inner ear.
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47
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Boya R, Yadavalli AD, Nikhat S, Kurukuti S, Palakodeti D, Pongubala JMR. Developmentally regulated higher-order chromatin interactions orchestrate B cell fate commitment. Nucleic Acids Res 2017; 45:11070-11087. [PMID: 28977418 PMCID: PMC5737614 DOI: 10.1093/nar/gkx722] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/09/2017] [Indexed: 12/17/2022] Open
Abstract
Genome organization in 3D nuclear-space is important for regulation of gene expression. However, the alterations of chromatin architecture that impinge on the B cell-fate choice of multi-potent progenitors are still unclear. By integrating in situ Hi-C analyses with epigenetic landscapes and genome-wide expression profiles, we tracked the changes in genome architecture as the cells transit from a progenitor to a committed state. We identified the genomic loci that undergo developmental switch between A and B compartments during B-cell fate determination. Furthermore, although, topologically associating domains (TADs) are stable, a significant number of TADs display structural alterations that are associated with changes in cis-regulatory interaction landscape. Finally, we demonstrate the potential roles for Ebf1 and its downstream factor, Pax5, in chromatin reorganization and transcription regulation. Collectively, our studies provide a general paradigm of the dynamic relationship between chromatin reorganization and lineage-specific gene expression pattern that dictates cell-fate determination.
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Affiliation(s)
- Ravi Boya
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Anurupa Devi Yadavalli
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Sameena Nikhat
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Sreenivasulu Kurukuti
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Dasaradhi Palakodeti
- Institute for Stem Cell Biology and Regenerative Medicine, National Centre for Biological Sciences, Bangalore 560065, India
| | - Jagan M R Pongubala
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
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48
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Sheth R, Barozzi I, Langlais D, Osterwalder M, Nemec S, Carlson HL, Stadler HS, Visel A, Drouin J, Kmita M. Distal Limb Patterning Requires Modulation of cis-Regulatory Activities by HOX13. Cell Rep 2017; 17:2913-2926. [PMID: 27974206 PMCID: PMC5697718 DOI: 10.1016/j.celrep.2016.11.039] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/08/2016] [Accepted: 11/11/2016] [Indexed: 01/12/2023] Open
Abstract
The combinatorial expression of Hox genes along the body axes is a major determinant of cell fate and plays a pivotal role in generating the animal body plan. Loss of HOXA13 and HOXD13 transcription factors (HOX13) leads to digit agenesis in mice, but how HOX13 proteins regulate transcriptional outcomes and confer identity to the distal-most limb cells has remained elusive. Here, we report on the genome-wide profiling of HOXA13 and HOXD13 in vivo binding and changes of the transcriptome and chromatin state in the transition from the early to the late-distal limb developmental program, as well as in Hoxa13−/−; Hoxd13−/−limbs. Our results show that proper termination of the early limb transcriptional program and activation of the late-distal limb program are coordinated by the dual action of HOX13 on cis-regulatory modules.
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Affiliation(s)
- Rushikesh Sheth
- Laboratory of Genetics and Development, Institut de Recherches Cliniques de Montréal (IRCM), 110 avenue des Pins Ouest, Montréal, QC H2W1R7, Canada.
| | - Iros Barozzi
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Langlais
- Department of Biochemistry, McGill University, 3649 Promenade Sir-William-Osler, Montréal, H3G0B1 QC, Canada
| | | | - Stephen Nemec
- Laboratory of Molecular Genetics, Institut de Recherches Cliniques de Montréal (IRCM), 110 avenue des Pins Ouest, Montréal, H2W1R7 QC, Canada
| | - Hanqian L Carlson
- Department of Skeletal Biology, Shriners Hospital for Children, 3101 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - H Scott Stadler
- Department of Skeletal Biology, Shriners Hospital for Children, 3101 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, CA 95340, USA
| | - Jacques Drouin
- Laboratory of Molecular Genetics, Institut de Recherches Cliniques de Montréal (IRCM), 110 avenue des Pins Ouest, Montréal, H2W1R7 QC, Canada; Department of Medicine, Université de Montréal, Montréal, H3T1J4 QC, Canada
| | - Marie Kmita
- Laboratory of Genetics and Development, Institut de Recherches Cliniques de Montréal (IRCM), 110 avenue des Pins Ouest, Montréal, QC H2W1R7, Canada; Department of Medicine, Université de Montréal, Montréal, H3T1J4 QC, Canada.
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49
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Benabdallah NS, Gautier P, Hekimoglu-Balkan B, Lettice LA, Bhatia S, Bickmore WA. SBE6: a novel long-range enhancer involved in driving sonic hedgehog expression in neural progenitor cells. Open Biol 2017; 6:rsob.160197. [PMID: 27852806 PMCID: PMC5133441 DOI: 10.1098/rsob.160197] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/20/2016] [Indexed: 12/14/2022] Open
Abstract
The expression of genes with key roles in development is under very tight spatial and temporal control, mediated by enhancers. A classic example of this is the sonic hedgehog gene (Shh), which plays a pivotal role in the proliferation, differentiation and survival of neural progenitor cells both in vivo and in vitro. Shh expression in the brain is tightly controlled by several known enhancers that have been identified through genetic, genomic and functional assays. Using chromatin profiling during the differentiation of embryonic stem cells to neural progenitor cells, here we report the identification of a novel long-range enhancer for Shh—Shh-brain-enhancer-6 (SBE6)—that is located 100 kb upstream of Shh and that is required for the proper induction of Shh expression during this differentiation programme. This element is capable of driving expression in the vertebrate brain. Our study illustrates how a chromatin-focused approach, coupled to in vivo testing, can be used to identify new cell-type specific cis-regulatory elements, and points to yet further complexity in the control of Shh expression during embryonic brain development.
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Affiliation(s)
- Nezha S Benabdallah
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.,Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Philippe Gautier
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Betul Hekimoglu-Balkan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Laura A Lettice
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Shipra Bhatia
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
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50
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Rodríguez-Carballo E, Lopez-Delisle L, Zhan Y, Fabre PJ, Beccari L, El-Idrissi I, Huynh THN, Ozadam H, Dekker J, Duboule D. The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes. Genes Dev 2017; 31:2264-2281. [PMID: 29273679 PMCID: PMC5769770 DOI: 10.1101/gad.307769.117] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 11/21/2017] [Indexed: 12/11/2022]
Abstract
The mammalian HoxD cluster lies between two topologically associating domains (TADs) matching distinct enhancer-rich regulatory landscapes. During limb development, the telomeric TAD controls the early transcription of Hoxd genes in forearm cells, whereas the centromeric TAD subsequently regulates more posterior Hoxd genes in digit cells. Therefore, the TAD boundary prevents the terminal Hoxd13 gene from responding to forearm enhancers, thereby allowing proper limb patterning. To assess the nature and function of this CTCF-rich DNA region in embryos, we compared chromatin interaction profiles between proximal and distal limb bud cells isolated from mutant stocks where various parts of this boundary region were removed. The resulting progressive release in boundary effect triggered inter-TAD contacts, favored by the activity of the newly accessed enhancers. However, the boundary was highly resilient, and only a 400-kb deletion, including the whole-gene cluster, was eventually able to merge the neighboring TADs into a single structure. In this unified TAD, both proximal and distal limb enhancers nevertheless continued to work independently over a targeted transgenic reporter construct. We propose that the whole HoxD cluster is a dynamic TAD border and that the exact boundary position varies depending on both the transcriptional status and the developmental context.
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Affiliation(s)
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ye Zhan
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Pierre J Fabre
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Leonardo Beccari
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Imane El-Idrissi
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Thi Hanh Nguyen Huynh
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Hakan Ozadam
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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